data_8DD0
#
_model_server_result.job_id            O0lEkGJrLJdVNgC4owvJ2w 
_model_server_result.datetime_utc      '2025-07-06 15:49:02' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          8dd0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":401}' 
#
_entry.id    8DD0 
#
_exptl.entry_id    8DD0 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexadecameric 
_pdbx_struct_assembly.oligomeric_count      16 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    ? 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 Q N N 
? 4 S N N 
? 4 U N N 
? 4 W N N 
? 4 Y N N 
? 4 AA N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OE1 GLN 139 A GLN 137 1_555 R MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? 
metalc ? metalc2 Q O1B ADP . A ADP 401 1_555 R MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? 
metalc ? metalc3 B OE1 GLN 139 B GLN 137 1_555 T MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? 
metalc ? metalc4 S O1B ADP . B ADP 401 1_555 T MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? 
metalc ? metalc5 C OE1 GLN 139 C GLN 137 1_555 V MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? 
metalc ? metalc6 U O1B ADP . C ADP 401 1_555 V MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? 
metalc ? metalc7 D OE1 GLN 139 D GLN 137 1_555 X MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? 
metalc ? metalc8 W O1B ADP . D ADP 401 1_555 X MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? 
metalc ? metalc9 E OE1 GLN 139 E GLN 137 1_555 Z MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? 
metalc ? metalc10 Y O1B ADP . E ADP 401 1_555 Z MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? 
metalc ? metalc11 F OE1 GLN 139 F GLN 137 1_555 BA MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? 
metalc ? metalc12 AA O1B ADP . F ADP 401 1_555 BA MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     8DD0 
_atom_sites.fract_transf_matrix[1][1]    1 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    1 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
Q 4 ADP A 1 401 401 ADP ADP . 
R 5 MG A 1 402 402 MG MG . 
S 4 ADP B 1 401 401 ADP ADP . 
T 5 MG B 1 402 402 MG MG . 
U 4 ADP C 1 401 401 ADP ADP . 
V 5 MG C 1 402 402 MG MG . 
W 4 ADP D 1 401 401 ADP ADP . 
X 5 MG D 1 402 402 MG MG . 
Y 4 ADP E 1 401 401 ADP ADP . 
Z 5 MG E 1 402 402 MG MG . 
AA 4 ADP F 1 401 401 ADP ADP . 
BA 5 MG F 1 402 402 MG MG . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 P PB ADP . . . AA 4 40.91 67.125 183.603 1 11.99 ? PB ADP 401 F 1 
HETATM 2 O O1B ADP . . . AA 4 41.305 66.976 182.16 1 11.99 ? O1B ADP 401 F 1 
HETATM 3 O O2B ADP . . . AA 4 40.089 68.348 183.894 1 11.99 ? O2B ADP 401 F 1 
HETATM 4 O O3B ADP . . . AA 4 40.419 65.867 184.264 1 11.99 ? O3B ADP 401 F 1 
HETATM 5 P PA ADP . . . AA 4 42.741 68.925 184.659 1 11.99 ? PA ADP 401 F 1 
HETATM 6 O O1A ADP . . . AA 4 43.031 69.627 183.367 1 11.99 ? O1A ADP 401 F 1 
HETATM 7 O O2A ADP . . . AA 4 41.795 69.501 185.662 1 11.99 ? O2A ADP 401 F 1 
HETATM 8 O O3A ADP . . . AA 4 42.284 67.422 184.362 1 11.99 ? O3A ADP 401 F 1 
HETATM 9 O O5' ADP . . . AA 4 44.121 68.649 185.405 1 11.99 ? O5' ADP 401 F 1 
HETATM 10 C C5' ADP . . . AA 4 44.262 68.925 186.789 1 11.99 ? C5' ADP 401 F 1 
HETATM 11 C C4' ADP . . . AA 4 45.58 68.303 187.206 1 11.99 ? C4' ADP 401 F 1 
HETATM 12 O O4' ADP . . . AA 4 46.637 69.045 186.616 1 11.99 ? O4' ADP 401 F 1 
HETATM 13 C C3' ADP . . . AA 4 45.786 68.337 188.697 1 11.99 ? C3' ADP 401 F 1 
HETATM 14 O O3' ADP . . . AA 4 45.601 67.021 189.214 1 11.99 ? O3' ADP 401 F 1 
HETATM 15 C C2' ADP . . . AA 4 47.222 68.755 188.878 1 11.99 ? C2' ADP 401 F 1 
HETATM 16 O O2' ADP . . . AA 4 47.999 67.597 189.176 1 11.99 ? O2' ADP 401 F 1 
HETATM 17 C C1' ADP . . . AA 4 47.675 69.301 187.547 1 11.99 ? C1' ADP 401 F 1 
HETATM 18 N N9 ADP . . . AA 4 47.801 70.762 187.677 1 11.99 ? N9 ADP 401 F 1 
HETATM 19 C C8 ADP . . . AA 4 46.773 71.61 187.781 1 11.99 ? C8 ADP 401 F 1 
HETATM 20 N N7 ADP . . . AA 4 47.202 72.887 187.895 1 11.99 ? N7 ADP 401 F 1 
HETATM 21 C C5 ADP . . . AA 4 48.536 72.859 187.865 1 11.99 ? C5 ADP 401 F 1 
HETATM 22 C C6 ADP . . . AA 4 49.608 73.863 187.942 1 11.99 ? C6 ADP 401 F 1 
HETATM 23 N N6 ADP . . . AA 4 49.326 75.179 188.075 1 11.99 ? N6 ADP 401 F 1 
HETATM 24 N N1 ADP . . . AA 4 50.873 73.424 187.877 1 11.99 ? N1 ADP 401 F 1 
HETATM 25 C C2 ADP . . . AA 4 51.153 72.122 187.747 1 11.99 ? C2 ADP 401 F 1 
HETATM 26 N N3 ADP . . . AA 4 50.232 71.154 187.669 1 11.99 ? N3 ADP 401 F 1 
HETATM 27 C C4 ADP . . . AA 4 48.928 71.457 187.726 1 11.99 ? C4 ADP 401 F 1 
#
_model_server_stats.io_time_ms              105 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#